[phenixbb] geometry of disulfide and NAG

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Jan 22 08:59:21 PST 2009


Li-Zhi

In addition to what Pavel said, the monomer library entry for NAG has 
N2, C7, O7 and C8 in a plane.  C2 is not necessarily in the same plane.

Nigel

On 1/22/09 7:06 AM, Li-Zhi Mi wrote:
> Hi,
>   I am using phenix to refine a low resolution structure. The problem I
> had is that the geometry of disulfide and NAG in the refined structure
> is not right. I did use a very tight geometry restrains. Both wxc_scale
> and wxu_scale are set to 0.05. In the refined structures, the sulfur of
> one cys is very close to the Cb of its disulfide partner. For NAG part,
> C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a
> way to adjust these violations?
>   Thanks in advance for the helps,
>   Li-Zhi Mi,
>
>
>
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>   

-- 
Nigel W. Moriarty
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Lawrence Berkeley National Laboratory
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Email : NWMoriarty at LBL.gov
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